iNOTE (version 1.0)

inote: Integrative Network Omnibus Total Effect Test

Description

Omnibus variance-component based testing procedure to test for the total effect of methylation loci and mRNA expression across a network without requiring the specification of an underlying disease risk model.

Usage

inote(iCPG, iGE, iY, iX, i.omniseed=NA, no.pert = 1000, imethod = "chi")

Arguments

iCPG

A list of J CpG matrices with dimensions nx\(p_{j}\).

iGE

An nxJ matrix of gene expression values.

iY

An nx1 dichotomous outcome vector.

iX

An nxr covariate matrix.

i.omniseed

A Jx1 seed vector.

no.pert

No. perturbations per gene level test; defaults to 1000.

imethod

Omnibus testing method -- 'chi' or 'uni'

Value

A list with the following components:

p

The omnibus test p-value for the joint, integrative total effect test for the gene set.

p.00

The null distribution of the omnibus test statistic p-value.

method

The omnibus method specified by the user.

gs.uni.mod

If applicable, the omnibus gene-set model selected by the iNOTE-uni method.

References

Chu S.H. and Huang Y-T. (2017) Integrative genomic analysis of biological gene sets with applications in lung cancer. (Revise and Resubmit)

Examples

data(X); data(Y); data(CPG); data(GE)
inote(iCPG=CPG, iGE=GE, iY=Y, iX=X, no.pert=1000, imethod='chi')